ArticleBMC genomics2017
Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Applications of omics in deciphering the unique traits of durian, the king of fruits.Plant molecular biology · 2026Review
- Complete genome of the Medicago anthracnose fungus,Microbial genomics · 2024Article
- Whole-genome sequencing of Ganoderma boninense, the causal agent of basal stem rot disease in oil palm, via combined short- and long-read sequencing.Scientific reports · 2024Article
- Genome assembly of Medicago truncatula accession SA27063 provides insight into spring black stem and leaf spot disease resistance.BMC genomics · 2024Article
- CRISPR/Cas9-Mediated Generation of Mutant Lines inBiology · 2024Article
- Gene-editedFrontiers in plant science · 2024Article
- Review
- MtING2 encodes an ING domain PHD finger protein which affects Medicago growth, flowering, global patterns of H3K4me3, and gene expression.The Plant journal : for cell and molecular biology · 2022Article
- Editorial: Functional Genomics in Plant Breeding 2.0.International journal of molecular sciences · 2022Article
- Alfalfa (Medicago sativa L.) pho2 mutant plants hyperaccumulate phosphate.G3 (Bethesda, Md.) · 2022Article
- Standardized genome-wide function prediction enables comparative functional genomics: a new application area for Gene Ontologies in plants.GigaScience · 2022Article
- Comparison of structural variants in the whole genome sequences of two Medicago truncatula ecotypes: Jemalong A17 and R108.BMC plant biology · 2022Article
- Delineating theInternational journal of molecular sciences · 2021Article
- A highly differentiated region of wheat chromosome 7AL encodes a Pm1a immune receptor that recognizes its corresponding AvrPm1a effector from Blumeria graminis.The New phytologist · 2021Article
- The Candidate Photoperiod GeneFrontiers in plant science · 2021Article
- A chromosome-scale genome assembly of a diploid alfalfa, the progenitor of autotetraploid alfalfa.Horticulture research · 2020Article
- A high-contiguity Brassica nigra genome localizes active centromeres and defines the ancestral Brassica genome.Nature plants · 2020Article
- The Position and Complex Genomic Architecture of Plant T-DNA Insertions Revealed by 4SEE.International journal of molecular sciences · 2020Article
- A Chromosome-Scale Assembly of the Garden Orach (Frontiers in plant science · 2020Article
- Advances in optical mapping for genomic research.Computational and structural biotechnology journal · 2020Review
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12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThird generation sequencing technologies, with sequencing reads in the tens- of kilo-bases, facilitate genome assembly by spanning ambiguous regions and improving continuity. This has been critical for plant genomes, which are difficult to assemble due to high repeat content, gene family expansions, segmental and tandem duplications, and polyploidy. Recently, high-throughput mapping and scaffolding strategies have further improved continuity. Together, these long-range technologies enable quality draft assemblies of complex genomes in a cost-effective and timely manner.
resultsHere, we present high quality genome assemblies of the model legume plant, Medicago truncatula (R108) using PacBio, Dovetail Chicago (hereafter, Dovetail) and BioNano technologies. To test these technologies for plant genome assembly, we generated five assemblies using all possible combinations and ordering of these three technologies in the R108 assembly. While the BioNano and Dovetail joins overlapped, they also showed complementary gains in continuity and join numbers. Both technologies spanned repetitive regions that PacBio alone was unable to bridge. Combining technologies, particularly Dovetail followed by BioNano, resulted in notable improvements compared to Dovetail or BioNano alone. A combination of PacBio, Dovetail, and BioNano was used to generate a high quality draft assembly of R108, a M. truncatula accession widely used in studies of functional genomics. As a test for the usefulness of the resulting genome sequence, the new R108 assembly was used to pinpoint breakpoints and characterize flanking sequence of a previously identified translocation between chromosomes 4 and 8, identifying more than 22.7 Mb of novel sequence not present in the earlier A17 reference assembly.
conclusionsAdding Dovetail followed by BioNano data yielded complementary improvements in continuity over the original PacBio assembly. This strategy proved efficient and cost-effective for developing a quality draft assembly compared to traditional reference assemblies.
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